Structure of PDB 4dct Chain A Binding Site BS01

Receptor Information
>4dct Chain A (length=401) Species: 1423 (Bacillus subtilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KPVVAIVGRPNVGKSTIFNIAGERISRIYSSAEWLNYDFNLIDTGGPFLA
QIRQQAEIAMDEADVIIFMVNGREGVTAADEEVAKILYRTKKPVVLAVNK
LNIYDFYSLGFGEPYPISGTHGLGLGDLLDAVAEHFKNIPETKYNEEVIQ
FCLIGRPNVGKSSLVNAMLGEERVIVSNDAVDTSFTYNQQEFVIVDTAGM
RKKGKVYETTEKYSVLRALKAIDRSEVVAVVLDGEEGIIEQDKRIAGYAH
EAGKAVVIVVNKWDAVDKDESTMKEFEENIRDHFQFLDYAPILFMSALTK
KRIHTLMPAIIKASENHSLRVQTNVLNDVIMDAVAMNPTPTHNGSRLKIY
YATQVSVKPPSFVVFVNDPELMHFSYERFLENRIRDAFGFEGTPIKIFAR
A
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain4dct Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4dct Potassium Acts as a GTPase-Activating Element on Each Nucleotide-Binding Domain of the Essential Bacillus subtilis EngA.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		N185 G187 K188 S189 S190 K236 N294 K295 D297 S329 A330 L331
Binding residue
(residue number reindexed from 1)		N158 G160 K161 S162 S163 K203 N261 K262 D264 S296 A297 L298
Annotation score4
Binding affinityMOAD: Kd=8uM
Enzymatic activity
Catalytic site (original residue number in PDB) F20 E26
Catalytic site (residue number reindexed from 1) F18 E23
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005525 GTP binding
GO:0043022 ribosome binding
Biological Process
GO:0042254 ribosome biogenesis

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4dct, PDBe:4dct, PDBj:4dct
PDBsum4dct
PubMed23056455
UniProtP50743|DER_BACSU GTPase Der (Gene Name=der)

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